Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011426.1 Corchorus capsularis cultivar CVL-1 contig11447, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:986 original size:36 final size:36
Alignment explanation
Indices: 938--1018 Score: 128
Period size: 36 Copynumber: 2.2 Consensus size: 36
928 TTATGTATTA
*
938 GGCGACCT-AGGCCAGCGGCGTTATAGCCAAACATTG
1 GGCGA-CTAAGGCCAGCGGCGTTATAGCCAAACATCG
*
974 GGCGACTAAGGCCAGCGGCGTTATAGCCAAGCATCG
1 GGCGACTAAGGCCAGCGGCGTTATAGCCAAACATCG
1010 GGCGACTAA
1 GGCGACTAA
1019 AACCAGCGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 2 0.05
36 40 0.95
ACGTcount: A:0.26, C:0.27, G:0.32, T:0.15
Consensus pattern (36 bp):
GGCGACTAAGGCCAGCGGCGTTATAGCCAAACATCG
Found at i:1025 original size:36 final size:36
Alignment explanation
Indices: 949--1026 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
939 GCGACCTAGG
* **
949 CCAGCGGCGTTATAGCCAAACATTGGGCGACTAAGG
1 CCAGCGGCGTTATAGCCAAACATCGGGCGACTAAAA
*
985 CCAGCGGCGTTATAGCCAAGCATCGGGCGACTAAAA
1 CCAGCGGCGTTATAGCCAAACATCGGGCGACTAAAA
1021 CCAGCG
1 CCAGCG
1027 ACATTACAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.28, G:0.29, T:0.14
Consensus pattern (36 bp):
CCAGCGGCGTTATAGCCAAACATCGGGCGACTAAAA
Found at i:2928 original size:16 final size:16
Alignment explanation
Indices: 2906--2994 Score: 112
Period size: 16 Copynumber: 5.6 Consensus size: 16
2896 GGAGAGTGTG
2906 GGTGAGTATCT-CACCA
1 GGTGAGTAT-TACACCA
*
2922 AGTGAGTATTACACCA
1 GGTGAGTATTACACCA
2938 GGTGAGTATCT-CACCA
1 GGTGAGTAT-TACACCA
2954 GGTGAGTATTACACCA
1 GGTGAGTATTACACCA
* *
2970 GGTGAGTATT-TACTA
1 GGTGAGTATTACACCA
2985 GGTGAGTATT
1 GGTGAGTATT
2995 GTACTGGGTG
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
15 15 0.23
16 50 0.76
17 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (16 bp):
GGTGAGTATTACACCA
Found at i:2997 original size:105 final size:105
Alignment explanation
Indices: 2879--3086 Score: 319
Period size: 105 Copynumber: 2.0 Consensus size: 105
2869 TGGCCTCACC
*
2879 AGGTGAGTATTGTATTGGGAGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGGTGAG
1 AGGTGAGTATTGTACTGGGAGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGGTGAG
*
2944 TATCTCACCAGGTGAGTA-TTACACCAGGTGAGTATTTACT
66 TAT-TCACCAAGTGAGTATTTACACCAGGTGAGTATTTACT
* * *
2984 AGGTGAGTATTGTACTGGGTGAGTGTGGGTGAGTATCTCACCAGGTGAGTATTGCACCAGGTGAG
1 AGGTGAGTATTGTACTGGGAGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGGTGAG
* * **
3049 TATTTACCAAGTGGGTATTTGTACCAGGTGAGTATTTA
66 TATTCACCAAGTGAGTATTTACACCAGGTGAGTATTTA
3087 TATTGGGTGA
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
104 11 0.12
105 82 0.88
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (105 bp):
AGGTGAGTATTGTACTGGGAGAGTGTGGGTGAGTATCTCACCAAGTGAGTATTACACCAGGTGAG
TATTCACCAAGTGAGTATTTACACCAGGTGAGTATTTACT
Found at i:3004 original size:16 final size:15
Alignment explanation
Indices: 2923--3007 Score: 71
Period size: 16 Copynumber: 5.4 Consensus size: 15
2913 ATCTCACCAA
* *
2923 GTGAGTATTACACCAG
1 GTGAGTATT-TACTAG
* *
2939 GTGAGTATCTCACCAG
1 GTGAGTAT-TTACTAG
* *
2955 GTGAGTATTACACCAG
1 GTGAGTATT-TACTAG
2971 GTGAGTATTTACTAG
1 GTGAGTATTTACTAG
*
2986 GTGAGTATTGTACTGG
1 GTGAGTATT-TACTAG
3002 GTGAGT
1 GTGAGT
3008 GTGGGTGAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.22
16 48 0.76
17 1 0.02
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (15 bp):
GTGAGTATTTACTAG
Found at i:3007 original size:31 final size:32
Alignment explanation
Indices: 2906--2994 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
2896 GGAGAGTGTG
*
2906 GGTGAGTATCTCACCAAGTGAGTATTACACCA
1 GGTGAGTATCTCACCAGGTGAGTATTACACCA
2938 GGTGAGTATCTCACCAGGTGAGTATTACACCA
1 GGTGAGTATCTCACCAGGTGAGTATTACACCA
* *
2970 GGTGAGTAT-TTACTAGGTGAGTATT
1 GGTGAGTATCTCACCAGGTGAGTATT
2995 GTACTGGGTG
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 14 0.26
32 40 0.74
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (32 bp):
GGTGAGTATCTCACCAGGTGAGTATTACACCA
Found at i:3032 original size:16 final size:16
Alignment explanation
Indices: 3011--3084 Score: 80
Period size: 16 Copynumber: 4.6 Consensus size: 16
3001 GGTGAGTGTG
3011 GGTGAGTATCT-CACCA
1 GGTGAGTAT-TGCACCA
3027 GGTGAGTATTGCACCA
1 GGTGAGTATTGCACCA
*
3043 GGTGAGTATT-TACCA
1 GGTGAGTATTGCACCA
* * *
3058 AGTGGGTATTTGTACCA
1 GGTGAGTA-TTGCACCA
3075 GGTGAGTATT
1 GGTGAGTATT
3085 TATATTGGGT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
15 11 0.22
16 28 0.56
17 11 0.22
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (16 bp):
GGTGAGTATTGCACCA
Found at i:3047 original size:42 final size:41
Alignment explanation
Indices: 2970--3049 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 41
2960 TATTACACCA
* * * **
2970 GGTGAGTATTTACTAGGTGAGTATTGTACTGGGTGAGTGTG
1 GGTGAGTATTCACCAGGTGAGTATTGCACCAGGTGAGTGTG
3011 GGTGAGTATCTCACCAGGTGAGTATTGCACCAGGTGAGT
1 GGTGAGTAT-TCACCAGGTGAGTATTGCACCAGGTGAGT
3050 ATTTACCAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
41 9 0.27
42 24 0.73
ACGTcount: A:0.21, C:0.11, G:0.36, T:0.31
Consensus pattern (41 bp):
GGTGAGTATTCACCAGGTGAGTATTGCACCAGGTGAGTGTG
Found at i:3067 original size:73 final size:74
Alignment explanation
Indices: 2938--3081 Score: 227
Period size: 73 Copynumber: 2.0 Consensus size: 74
2928 TATTACACCA
* * **
2938 GGTGAGTATCTCACCAGGTGAGTATTACACCAGGTGAGTATTTACTAGGTGAGTA-TTGTACTGG
1 GGTGAGTATCTCACCAGGTGAGTATTACACCAGGTGAGTATTTACCAAGTGAGTATTTGTACCAG
3002 GTGAGTGTG
66 GTGAGTGTG
* *
3011 GGTGAGTATCTCACCAGGTGAGTATTGCACCAGGTGAGTATTTACCAAGTGGGTATTTGTACCAG
1 GGTGAGTATCTCACCAGGTGAGTATTACACCAGGTGAGTATTTACCAAGTGAGTATTTGTACCAG
3076 GTGAGT
66 GTGAGT
3082 ATTTATATTG
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
73 51 0.80
74 13 0.20
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.31
Consensus pattern (74 bp):
GGTGAGTATCTCACCAGGTGAGTATTACACCAGGTGAGTATTTACCAAGTGAGTATTTGTACCAG
GTGAGTGTG
Found at i:3075 original size:32 final size:31
Alignment explanation
Indices: 2907--3086 Score: 99
Period size: 32 Copynumber: 5.9 Consensus size: 31
2897 GAGAGTGTGG
* * *
2907 GTGAGTATCT-CACCAAGTGAGTATTACACCAG
1 GTGAGTAT-TGCACCAGGTGAGTATT-TACCAA
* *
2939 GTGAGTATCT-CACCAGGTGAGTATTACACCAG
1 GTGAGTAT-TGCACCAGGTGAGTATT-TACCAA
* * ***
2971 GTGAGTATT-TACTAGGTGAGTATTGTACTGG
1 GTGAGTATTGCACCAGGTGAGTATT-TACCAA
* * *
3002 GTGAGT-GTG-----GGTGAGTATCTCACCAG
1 GTGAGTATTGCACCAGGTGAGTAT-TTACCAA
3028 GTGAGTATTGCACCAGGTGAGTATTTACCAA
1 GTGAGTATTGCACCAGGTGAGTATTTACCAA
* *
3059 GTGGGTATTTGTACCAGGTGAGTATTTA
1 GTGAGTA-TTGCACCAGGTGAGTATTTA
3087 TATTGGGTGA
Statistics
Matches: 123, Mismatches: 16, Indels: 18
0.78 0.10 0.11
Matches are distributed among these distances:
26 18 0.15
27 3 0.02
30 1 0.01
31 34 0.28
32 67 0.54
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.31
Consensus pattern (31 bp):
GTGAGTATTGCACCAGGTGAGTATTTACCAA
Found at i:4497 original size:146 final size:147
Alignment explanation
Indices: 4312--4583 Score: 392
Period size: 146 Copynumber: 1.9 Consensus size: 147
4302 CACGCTATTT
* * *
4312 TGGTTTCCCTCTCGTTTTTTTCCGTGCAAAATTAGAAAATTAGCTT-AAAATTAACTATAACGGT
1 TGGTTTCCCTCTCGTTTTTTTCCGCGCAAAATTAGAAAATTA-CTTGAAAATTAACTATAACAGC
* * *
4376 GTTTGTTATTTG-GAACGCCATAATAGTTGTTAGTATGGA-GGCGTTTGTACTTAAAAACGCCGC
65 GTTTGTTA-TTGAAAACGCCATAATAATTGTTAGTAT-AACGGCGTTTGTACTTAAAAACGCCGC
4439 CATCATTAAGGCAAAACTTA
128 CATCATTAAGGCAAAACTTA
* *
4459 TGGTTTCCCTTTC-TTTTTTTTCGCGCAAAATT-GAAAAATTACTTGAAAATTAACTATAACAGC
1 TGGTTTCCCTCTCGTTTTTTTCCGCGCAAAATTAG-AAAATTACTTGAAAATTAACTATAACAGC
*
4522 GTTTGTTATTGAAAACGCCATAATAATTGTTAGTGTAACGGCGTTTGTACTTAAAAACGCCG
65 GTTTGTTATTGAAAACGCCATAATAATTGTTAGTATAACGGCGTTTGTACTTAAAAACGCCG
4584 TAATTGTGTC
Statistics
Matches: 112, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
145 8 0.07
146 92 0.82
147 12 0.11
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (147 bp):
TGGTTTCCCTCTCGTTTTTTTCCGCGCAAAATTAGAAAATTACTTGAAAATTAACTATAACAGCG
TTTGTTATTGAAAACGCCATAATAATTGTTAGTATAACGGCGTTTGTACTTAAAAACGCCGCCAT
CATTAAGGCAAAACTTA
Found at i:4845 original size:26 final size:26
Alignment explanation
Indices: 4789--4845 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
4779 TTGACACATT
**
4789 TAAATTGGTAGTTTTTTTATTTCAAA
1 TAAATTGGTAGTTTTTTTAAATCAAA
* * *
4815 AAAATTGGTAGTTTTTTTAAATGATA
1 TAAATTGGTAGTTTTTTTAAATCAAA
4841 TAAAT
1 TAAAT
4846 AAAAATTAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (26 bp):
TAAATTGGTAGTTTTTTTAAATCAAA
Found at i:7612 original size:3 final size:3
Alignment explanation
Indices: 7606--7642 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
7596 AAAAAAAAGA
7606 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
7643 TCGATTCTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:11177 original size:17 final size:16
Alignment explanation
Indices: 11137--11185 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
11127 CATGTAATCT
*
11137 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
11153 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
11170 TTAGATCACTAGTGAT
1 TT-GATCACTGGTGAT
11186 TTGGAGGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:11466 original size:24 final size:25
Alignment explanation
Indices: 11437--11494 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
11427 CCATAATTTA
*
11437 TCTTTTCTTTTTCCTTCCT-TTTCT
1 TCTTTTCTTTTTCCTTCCTCTATCT
* * *
11461 TCTTTT-TATTTCTTTTCTCTATCT
1 TCTTTTCTTTTTCCTTCCTCTATCT
11485 TCTTTTCTTT
1 TCTTTTCTTT
11495 CTCTTCCGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 9 0.33
24 16 0.59
25 2 0.07
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.72
Consensus pattern (25 bp):
TCTTTTCTTTTTCCTTCCTCTATCT
Found at i:12754 original size:38 final size:38
Alignment explanation
Indices: 12710--12786 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
12700 TATTTTTTTT
*
12710 CCAATTATAAATTTATCTATATCTATAGTAATTTGCCA
1 CCAATTATAAATCTATCTATATCTATAGTAATTTGCCA
*
12748 CCAATTATATATCTATCTATATCTATAGTAATTTGCCA
1 CCAATTATAAATCTATCTATATCTATAGTAATTTGCCA
12786 C
1 C
12787 GTGTTTCACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (38 bp):
CCAATTATAAATCTATCTATATCTATAGTAATTTGCCA
Found at i:14512 original size:330 final size:321
Alignment explanation
Indices: 13325--14566 Score: 1030
Period size: 330 Copynumber: 3.8 Consensus size: 321
13315 GTGATGGTTA
* * * * * *
13325 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGGCCCGAAAGATATTTCCTCAATTTTTGGCTA
1 GTACACGATTTC-ACTAAAATTTTGCAAAAATTGACCCGAAATAT-TTTTCTCAATTTTTAGCCA
* * * * * * *
13390 AAATACTCATAAAAATATATATAATT-CAATCAAAAATATTGAAGGGA-TTTTAATGCTAT-TAA
64 CAATACTCAT-AAAATATATATAATTGAAAGCCAAAA-ATGGAA--GACTTTTCACGCT-TCTAA
* * * *
13452 TATCGTTTTCCTATTTTTCCCGAATTAATTTTTAATTAAATCAAAACAA-AGTTCAGATGCTTGT
124 TATCGTTTTCATATTTTT-CCAAATTAATTTCTAATTAAATCAAAACAAGA-TTCAGATGCTCGT
* * *** * *
13516 AAAAACAAATCCTTAAATATAATATTTTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAG
187 AAAAACAAATCCTTAAATACAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAC
* * * ***
13581 TATTGACACCAAAAATCATGCAAAACTGAGCCAA-ACACCGGAACACGTTTTTA-GCCGAAAA-C
252 TATTGACACCAAAAATCATGCAAAACTGA-CTAAGGCCCCGGAACACGTTTTTAGGTAAAAAACC
13643 GTGATGG
316 GTGAT-G
* * ** *
13650 TTAGTACATGATTTCAGCTAAAATTTTGCAAAAAATTGACCCGAAAGATTTTTTCTTGATTTCTA
1 ---GTACACGATTTCA-CTAAAATTTTGC-AAAAATTGACCCGAAATA-TTTTTCTCAATTTTTA
** * * ** * *
13715 GAGAAAATACTCATAAAAATATATATAATTGAAGGGGAAAAATTGAAAGTCTTTTTTCACGCTTC
60 GCCACAATACTCAT-AAAATATATATAATTGAAAGCCAAAAA-TGGAAGAC--TTTTCACGCTTC
* * * * * **
13780 TAATATCGTTTTTCTTATTTTATTTCCAAATTAATTTCTGATTAAATCGAACCAAGATTTAGAAA
121 TAATATCG-TTTTC--ATATT-TTTCCAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATG
* * *
13845 CTCATAAAAACAAATCCTTAAATACAATGTGGCTGAA-AATTGGTTAAATGAATATAGATATATT
182 CTCGTAAAAACAAATCCTTAAATACAATGTGGCT-AAGATTTGGTTAGATGAATATAG--ATATT
* * * * * * * *
13909 TTAAGGACTCTTGGCACTAAAAATCATGCAAAACTGACTCAGGTTCCCGGAACGCGTTTTTAGCT
244 TCAAGGACTATTGACACCAAAAATCATGCAAAACTGACTAAGG-CCCCGGAACACGTTTTTAGGT
*
13974 AATAAAACCATGATG
308 AA-AAAACCGTGATG
* * *
13989 GTACACGATTTCAACAAAAATTTTGCAAAAATTGACCCGAAATATTTTTCTCAATATTTAGCTAC
1 GTACACGATTTC-ACTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCTCAATTTTTAGCCAC
* * * **
14054 AATACTTATAAAA-ACTATATAATTCAAAGCCAAAAATATTGAAGGGTTTCTCACGCTTCTAATA
65 AATACTCATAAAATA-TATATAATTGAAAGCC-AAAA-ATGGAAGACTTT-TCACGCTTCTAATA
* * * * * * *
14118 TCGTTTTCCTATTTTTTTTCAAATTAATTTCTAAATAGATC-GAACATGATTCAAATGCTCGTAA
126 TCGTTTT-C-ATATTTTTCCAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAA
* * *
14182 AAGA-AAATCCTTAAATCCAATGTTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGATT
189 AA-ACAAATCCTTAAATACAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACT
* ** * * * *
14246 TTTTCCACCAAAAATCATACAAAACGGACTGAAGGCCCCGAAACACATTTTTAGGTAAAAAACCG
253 ATTGACACCAAAAATCATGCAAAACTGACT-AAGGCCCCGGAACACGTTTTTAGGTAAAAAACCG
14311 TGATG
317 TGATG
* * *
14316 GTACACGACTTCGACTAAAATTTTTACAAAAATTGACCCGAAATATTTTTCCTCAATTTTTACCC
1 GTACACGATTTC-ACTAAAA-TTTTGCAAAAATTGACCCGAAATATTTTT-CTCAATTTTTAGCC
* * * * *
14381 ACAACACTCATAAAATATATATAATTGAACGCCAACAAGATGGGGAGACTTTTCACACTTTTTAA
63 ACAATACTCATAAAATATATATAATTGAAAGCCAA-AA-AT-GGAAGACTTTTCACGC-TTCTAA
* ** * *
14446 TATTGTTTGTCATATTTTTCTGAATTAATTTCTAATTATATCAAAACAAGATTCAGATTCTCGTA
124 TATCGTTT-TCATATTTTTCCAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTA
* * * * *
14511 AAAACAAATCCTTAATTTCAATGTGGCTGAGATTTGATTAGATGAATCATAAATAT
188 AAAACAAATCCTTAAATACAATGTGGCTAAGATTTGGTTAGATGAAT-ATAGATAT
14567 AGATATTTCA
Statistics
Matches: 732, Mismatches: 141, Indels: 79
0.77 0.15 0.08
Matches are distributed among these distances:
327 28 0.04
328 108 0.15
329 134 0.18
330 144 0.20
331 47 0.06
332 19 0.03
333 34 0.05
334 108 0.15
335 25 0.03
336 59 0.08
337 16 0.02
339 5 0.01
340 5 0.01
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (321 bp):
GTACACGATTTCACTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCTCAATTTTTAGCCACA
ATACTCATAAAATATATATAATTGAAAGCCAAAAATGGAAGACTTTTCACGCTTCTAATATCGTT
TTCATATTTTTCCAAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAA
TCCTTAAATACAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTATTGACAC
CAAAAATCATGCAAAACTGACTAAGGCCCCGGAACACGTTTTTAGGTAAAAAACCGTGATG
Found at i:14604 original size:664 final size:660
Alignment explanation
Indices: 13325--14607 Score: 1412
Period size: 664 Copynumber: 1.9 Consensus size: 660
13315 GTGATGGTTA
** * * * *
13325 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGGCCCGAAAGATATTTCCTCAATTTTTGGCTA
1 GTACACGATTTCAACAAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATATTTAGCTA
* *
13390 AAATACTCATAAAAATATATATAATTCAATCAAAAATATTGAAGGGATTTTAATGCTATTAATAT
66 AAATACTCATAAAAATATATATAATTCAACCAAAAATATTGAAGGGATTTTAACGCTATTAATAT
* * * * *
13455 CGTTTTCCTATTTTTCCCGAATTAATTTTTAATTAAATCAAAACAAAGTTCAGATGCTTGTAAAA
131 CGTTTTCCTATTTTTCCCAAATTAATTTCTAAATAAATCAAAACAAAGTTCAAATGCTCGTAAAA
* ** *
13520 ACAAATCCTTAAATATAATATTTTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTATT
196 ACAAATCCTTAAATACAATATTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTATT
* * * * **
13585 GACACCAAAAATCATGCAAAACTGAGCCAAACACCGGAACACGTTTTTAGCCGAAAACGTGATGG
261 GACACCAAAAATCATACAAAACGGAGCCAAACACCGAAACACATTTTTAGCAAAAAACGTGATGG
* * * * **
13650 TTAGTACATGATTTCAGCTAAAATTTTGCAAAAAATTGACCCGAAAGATTTTTTCTTGATTTCTA
326 -T-GTACACGACTTCAGCTAAAATTTTACAAAAAATTGACCCGAAAGATTTTTCCTCAATTTCTA
* * * * ** * * *
13715 GAGAAAATACTCATAAAAATATATATAATTGAAGGGGAAAAATTGAAAGTCTTTTTTCACGCTTC
389 CACAAAACACTCATAAAAATATATATAATTGAACGCCAAAAATGGAAAGAC-TTTTTCACACTTC
* * * * * *
13780 TAATATCGTTTTTCTTATTTTATTTCCAAATTAATTTCTGATTAAATCGAACCAAGATTTAGAAA
453 TAATATCGTTTGTC-TATATTATTTCCAAATTAATTTCTAATTAAATCAAAACAAGATTCAGAAA
* *
13845 CTCATAAAAACAAATCCTTAAATACAATGTGGCTGAAAATTGGTTAAATGAATATAGATATATTT
517 CTCATAAAAACAAATCCTTAAATACAATGTGGCTGAAAATTGATTAAATGAATATAAATATATTT
* *
13910 TAAGGACTCTTGGCACTAAAAATCATGCAAAACTGACTCAGGTTCCCGGAACGCGTTTTTAGCTA
582 TAAGGAATCTCGGCACTAAAAATCATGCAAAACTGACTCAGGTTCCCGGAACGCGTTTTTAGCTA
13975 ATAAAACCATGATG
647 ATAAAACCATGATG
* *
13989 GTACACGATTTCAACAAAAATTTTGCAAAAATTGACCCGAAATAT-TTTTCTCAATATTTAGCTA
1 GTACACGATTTCAACAAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATATTTAGCTA
* * * *
14053 CAATACTTATAAAAA-CTATATAATTCAAAGCCAAAAATATTGAAGGG-TTTCTCACGCT-TCTA
66 AAATACTCATAAAAATATATATAATTC-AA-CCAAAAATATTGAAGGGATTT-TAACGCTAT-TA
** * * *
14115 ATATCGTTTTCCTATTTTTTTTCAAATTAATTTCTAAATAGATC-GAAC-ATGATTCAAATGCTC
127 ATATCGTTTTCCTA-TTTTTCCCAAATTAATTTCTAAATAAATCAAAACAAAG-TTCAAATGCTC
* *
14178 GTAAAAGA-AAATCCTTAAATCCAATGTTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAG
190 GTAAAA-ACAAATCCTTAAATACAATATTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAG
* * ** * * * *
14242 GATTTTTTCCACCAAAAATCATACAAAACGGA-CTGAAGGCCCCGAAACACATTTTTAGGTAAAA
254 GAGTATTGACACCAAAAATCATACAAAACGGAGC-CAA-ACACCGAAACACATTTTTA-GCAAAA
*
14306 AACCGTGAT-G-GTACACGACTTC-GACTAAAATTTTTAC-AAAAATTGACCCGAAATATTTTTC
316 AA-CGTGATGGTGTACACGACTTCAG-CTAAAA-TTTTACAAAAAATTGACCCGAAAGATTTTTC
* * * **
14367 CTCAATTTTTACCCACAACACTCAT-AAAATATATATAATTGAACGCCAACAAGATGGGGAGAC-
378 CTCAATTTCTACACAAAACACTCATAAAAATATATATAATTGAACGCCAA-AA-ATGGAAAGACT
* * ** *
14430 TTTTCACACTTTTTAATATTGTTTGTC-ATATT-TTTCTGAATTAATTTCTAATTATATCAAAAC
441 TTTTCACAC-TTCTAATATCGTTTGTCTATATTATTTCCAAATTAATTTCTAATTAAATCAAAAC
** * * * * * *
14493 AAGATTCAGATTCTCGTAAAAACAAATCCTTAATTTCAATGTGGCTGAGATTTGATTAGATGAAT
505 AAGATTCAGAAACTCATAAAAACAAATCCTTAAATACAATGTGGCTGAAAATTGATTAAATGAAT
* *
14558 CATAAATATAGATATTTCAAGGAATCTCGGCGC-AAAAATTATGCAAAACT
570 -ATAAATAT--AT-TTT-AAGGAATCTCGGCACTAAAAATCATGCAAAACT
14608 AAGCTAGGAC
Statistics
Matches: 508, Mismatches: 90, Indels: 42
0.79 0.14 0.07
Matches are distributed among these distances:
660 80 0.16
661 11 0.02
662 40 0.08
663 111 0.22
664 203 0.40
665 51 0.10
666 6 0.01
667 6 0.01
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (660 bp):
GTACACGATTTCAACAAAAATTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATATTTAGCTA
AAATACTCATAAAAATATATATAATTCAACCAAAAATATTGAAGGGATTTTAACGCTATTAATAT
CGTTTTCCTATTTTTCCCAAATTAATTTCTAAATAAATCAAAACAAAGTTCAAATGCTCGTAAAA
ACAAATCCTTAAATACAATATTGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTATT
GACACCAAAAATCATACAAAACGGAGCCAAACACCGAAACACATTTTTAGCAAAAAACGTGATGG
TGTACACGACTTCAGCTAAAATTTTACAAAAAATTGACCCGAAAGATTTTTCCTCAATTTCTACA
CAAAACACTCATAAAAATATATATAATTGAACGCCAAAAATGGAAAGACTTTTTCACACTTCTAA
TATCGTTTGTCTATATTATTTCCAAATTAATTTCTAATTAAATCAAAACAAGATTCAGAAACTCA
TAAAAACAAATCCTTAAATACAATGTGGCTGAAAATTGATTAAATGAATATAAATATATTTTAAG
GAATCTCGGCACTAAAAATCATGCAAAACTGACTCAGGTTCCCGGAACGCGTTTTTAGCTAATAA
AACCATGATG
Found at i:16254 original size:332 final size:332
Alignment explanation
Indices: 15524--17759 Score: 1189
Period size: 332 Copynumber: 6.7 Consensus size: 332
15514 GGGGGCCCGA
* ** * * ** * * **
15524 AACGCGTTTTTAGCAAAAAACGATGATGGTTAAAACACGATTTCGACTAAAATTTTACAAAAAAA
1 AACGCATTTTTAGCAAAAAAAAACGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATT
* * * ** * *
15589 TGA-CCATAAATTTTTTTCCT-AAATTTTTGCCTAAAACCCTCATGAAATATATATAATTTAACG
66 TGACCCA-AAATTATTTTCCTCAAATTTTAGCC-ACAATACTCAT-AAAAATATATAATTCAACG
* * * * * * *
15652 CCAAAAATAATGGAGGACTTTTCATGCTTTTCATATCGTTTTTCATACTTTGTCTGAATTAATTT
128 CCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATACTTTTTCTGAATTAATTT
* * * * * **
15717 CTGATTAAATTGAAACAATATTCAGATGCTCGTTAAAACAAATCCTCAAATGCAATGTGGTTGAG
193 CTAATTAAATCGAAACAAGATTCAGATGCTCGCTAAAACAAATCCTCAAATCCAATGTGACTGAG
*
15782 ATTTGATTAGATGAATATAGATATCTTAAGGAGACTTAGCGCAAAAAATCATGCAAAACTGACCC
258 ATTTGATTAGATGAATATAGATATCTTAAGGAGACTTAGCGCAAAAAATCACGCAAAACTGACCC
15847 GAGGCCGTGG
323 GAGGCCGTGG
* *** *
15857 AACGCATTTTTAGCCAAAAACCGCGATGATTATTACATGATTTCGGCTAAAATTTTGCAAAAATT
1 AACGCATTTTTAGCAAAAAAAAACGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATT
** * * ** *
15922 T-ATCGGAAAGA-TA-TTTCCTCAATTTTTGGTTA-AATGGCTCATTAAAAATATATAATTCAAC
66 TGA-CCCAAA-ATTATTTTCCTCAAATTTTAGCCACAAT-ACTCA-TAAAAATATATAATTCAAC
* * * * *
15983 GTCAAAAATATTGAAGGGGTTTTTACGCTTCTAATATCGTTTTTCCTACTTTTTCCGAATTAATT
127 GCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATACTTTTTCTGAATTAATT
* * *
16048 TCTAATTAAATCGAAACAAGATTTAGATGCTC-CTAAAA-AAATTCTTAAATCCAATGTGACTGA
192 TCTAATTAAATCGAAACAAGATTCAGATGCTCGCTAAAACAAATCCTCAAATCCAATGTGACTGA
* * *
16111 GATTTGATTAGATGAATATAGATAT-TTCAAGGAGTCTTGGCG-ATAAAAATCACGCAAAACTTA
257 GATTTGATTAGATGAATATAGATATCTT-AAGGAGACTTAGCGCA-AAAAATCACGCAAAACTGA
* * *
16174 CCCGGGGTCTTGG
320 CCCGAGGCCGTGG
* * * *
16187 AACGCGTTTTTAGCTAAAAAAAAAAAACTG-TGA-TGTTGCACGATTTCGGCTAATATTTTGC-A
1 AACGCATTTTTAGC----AAAAAAAAAC-GATGATTATTACACGATTTCGGCTAAAATTTTGCAA
* *
16249 AAATTTGACCCAAAATTATTTTCCTCAAATTTTAGCCACAATACTCA-AAAAATATATAACTGAA
61 AAATTTGACCCAAAATTATTTTCCTCAAATTTTAGCCACAATACTCATAAAAATATATAATTCAA
* * * * **
16313 CACCAAAAACATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTTTAATTTTTTTTCTGAATTA
126 CGCCAAAAATATTGAAGGGCTTTTCACGCTTCTAATATCG--TTTTTCATACTTTTTCTGAATTA
* * ** * *
16378 ATTTCTAATTAAAACAAAACATCATTCAGTTGCTTG-T------AA-----AAA---AATG-G-C
189 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCTAAAACAAATCCTCAAATCCAATGTGAC
* * * ** * * * ** *
16426 TGGGATTTGGTTAGATGAATATAGATATTTTAAGGATTC-TCGACACCAAAAATCATTCAAAATT
254 TGAGATTTGATTAGATGAATATAGATATCTTAAGGAGACTTAG-CGCAAAAAATCACGCAAAACT
** **
16490 GAATCG-GGCC-TCAA
318 GACCCGAGGCCGT-GG
** * **** * * *
16504 AACGTGTTTTTA-CACAAATACTGTGACGATTATTACATGATTTCGGCTAAACTTTTGCAAAAA-
1 AACGCATTTTTAGCA-AAAAAAAACGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAAT
* * * * *
16567 TTGACCCGAACCA-TA-TTTGCTCAATTTTTAGCCATAATACTCAATAAAAAATATATATTTCAA
65 TTGACCC-AA-AATTATTTTCCTCAAATTTTAGCCACAATACTC-AT-AAAAATATATAATTCAA
* * * ** *
16630 TGCCAGAAAA-ATTGATGGGCTTTTCACGCTTTTAATATTATTTTTCATAATTTTTTCTGAATTA
126 CGCCA-AAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCAT-ACTTTTTCTGAATTA
* * * * *
16694 ATTTCTAATTAAATTGAAACAAGATTCAGATGCTC-ATAGAAACAAATCCTTAAATGCAATGTGG
189 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCTA-AAACAAATCCTCAAATCCAATGTGA
* * * * * * **
16758 CTAAGATTTTATTAGATGGATATAGATAT-TTCAAGGAG--TGTCGCGCCAAAAATAATTCAAAA
253 CTGAGATTTGATTAGATGAATATAGATATCTT-AAGGAGACT-TAGCGCAAAAAATCACGCAAAA
* * * ****
16820 TTGA-ACGGGGCCCCAA
316 CTGACCCGAGGCCGTGG
* * * **** * * * *
16836 AATGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACAATTTTGGCTAAAATTTTGCCAAAAA-
1 AACGCATTTTTAGCAAAAAAAAACGATGATTATTACACGATTTCGGCTAAAATTTTG-CAAAAAT
* * * * * * ** *
16900 ATGACCTGAAAAAT-TTTTGCTCAATTTTTGGATAAAATACTCATAATATATATATATATATATA
65 TTGACC-CAAAATTATTTTCCTCAAATTTTAGCCACAATACTC-----ATA-A-A-A-ATATATA
* * * * * * *
16964 ATTTAACGTCAATAATATTTGAAGAG-TTTTCATGCTTTTAATATCATTTTTCATA-TTTTTCTG
120 ATTCAACGCCAAAAATA-TTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATACTTTTTCTG
** * * * *
17027 AATTAATTTCCGATTAAAACGAAACAAGATTCAGATGCTTG-TAAAAGCAAATTCTTAAATCCAA
184 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCTAAAA-CAAATCCTCAAATCCAA
* * * * * * * * * * *
17091 TGTGGCTGAGATTTAATTAGATGATTATGGATATCTCAAGGAGTCCTAACCCCAAAAAT-ATGCA
248 TGTGACTGAGATTTGATTAGATGAATATAGATATCTTAAGGAGACTTAGCGCAAAAAATCACGCA
* * ****
17155 AAACTGAGCCGGGGCCCCAT
313 AAACTGACCCGAGGCCGTGG
* * * **** * * * * *
17175 AACGCTTTTTTATCCAAAAACTGTGATGGTTATTACATGATTTCGACTAAAATTTTG-TAAAAGT
1 AACGCATTTTTAGCAAAAAAAAACGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATT
* * * * * *
17239 TGACCCAAAA-GATATTTCTTTAATTTTTTGCTGA-AATACTCATAAAAAGTATATAATTCAACG
66 TGACCCAAAATTAT-TTTCCTCAAATTTTAGC-CACAATACTCATAAAAA-TATATAATTCAACG
** * * * * * *
17302 CCAAAAGGATTGAAGGGGGTTTTGACGTTTCTAATATCGTTTCTCATATTTTTTCTAAATTAATT
128 CCAAAAATATTGAA-GGGCTTTTCACGCTTCTAATATCGTTTTTCATACTTTTTCTGAATTAATT
* *
17367 TCGAATTAAATCGAAACAAGATTCAGATGC-CG-TAAAAAGCAAATCCTTAAATCCAATGTGACT
192 TCTAATTAAATCGAAACAAGATTCAGATGCTCGCT-AAAA-CAAATCCTCAAATCCAATGTGACT
* * * * * * *
17430 GAGATTTGATTAGATGAATAGAGACAAT-TGAAGTAG-CTAGTATCGGAGTCAAAAATCATGCAA
255 GAGATTTGATTAGATGAATATAGA-TATCTTAAGGAGACT--TAGCGCA---AAAAATCACGCAA
* * ***
17493 AATTGAGCCG-GGTCCCCAG
314 AACTGACCCGAGG-CCGTGG
* * * * * *
17512 AACGCGTTTTTTGCCAAAAAAACCGTGATGGTTTGTTACTTGTTAGTACACGATTTCGCCTAAAA
1 AACGCATTTTTAGCAAAAAAAAAC--GA-----TG--A----TTATTACACGATTTCGGCTAAAA
* * * * * *
17577 -TTTGACAAAAA-TTGACACGAAA-TATTTCTCCTCAATTTTTGGCTAAAATACTCA-AGAAAAT
53 TTTTG-CAAAAATTTGACCCAAAATTATTT-TCCTCAAATTTTAGCCACAATACTCATA-AAAAT
* * * * * *
17638 ATATAATTCAATGCCAAAAATATTGGAA-GGCTTTTTACGCTTTTAATATCGTATTTCTTATTTT
115 ATATAATTCAACGCCAAAAATATT-GAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATA-CTT
*
17702 TTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG-TAGAAACAAAT
178 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGCTA-AAACAAAT
17760 TCTTAATTTC
Statistics
Matches: 1504, Mismatches: 281, Indels: 220
0.75 0.14 0.11
Matches are distributed among these distances:
312 2 0.00
313 6 0.00
314 54 0.04
315 16 0.01
316 46 0.03
317 58 0.04
318 56 0.04
319 3 0.00
320 4 0.00
323 5 0.00
328 5 0.00
329 9 0.01
330 118 0.08
331 90 0.06
332 292 0.19
333 233 0.15
334 14 0.01
335 1 0.00
336 9 0.01
337 52 0.03
338 130 0.09
339 77 0.05
340 41 0.03
341 6 0.00
344 2 0.00
348 25 0.02
349 82 0.05
350 64 0.04
351 4 0.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (332 bp):
AACGCATTTTTAGCAAAAAAAAACGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATT
TGACCCAAAATTATTTTCCTCAAATTTTAGCCACAATACTCATAAAAATATATAATTCAACGCCA
AAAATATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATACTTTTTCTGAATTAATTTCTA
ATTAAATCGAAACAAGATTCAGATGCTCGCTAAAACAAATCCTCAAATCCAATGTGACTGAGATT
TGATTAGATGAATATAGATATCTTAAGGAGACTTAGCGCAAAAAATCACGCAAAACTGACCCGAG
GCCGTGG
Found at i:18161 original size:15 final size:16
Alignment explanation
Indices: 18143--18172 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18133 ATAAATAATA
18143 ATATTATAA-CTAAAT
1 ATATTATAATCTAAAT
18158 ATATTATAATCTAAA
1 ATATTATAATCTAAA
18173 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:19420 original size:21 final size:22
Alignment explanation
Indices: 19359--19420 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
19349 TATTTTGATA
*
19359 TAAT-ATTATTATTTCTAAATTTT
1 TAATAATTA-TATTT-TATATTTT
* *
19382 TAATAA-TATATATAATATTTT
1 TAATAATTATATTTTATATTTT
19403 TAA-AATTATATTTTATAT
1 TAATAATTATATTTTATAT
19421 ATATTGTAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 2 0.06
21 19 0.59
22 4 0.12
23 6 0.19
24 1 0.03
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TAATAATTATATTTTATATTTT
Found at i:19537 original size:18 final size:17
Alignment explanation
Indices: 19510--19547 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
19500 TTTCGGTTAA
19510 ACCCGCTTAACCGACCGC
1 ACCCGCTTAACCGACC-C
*
19528 ACCCGTTTAACCGACCC
1 ACCCGCTTAACCGACCC
19545 ACC
1 ACC
19548 ATGGATGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.24, C:0.50, G:0.13, T:0.13
Consensus pattern (17 bp):
ACCCGCTTAACCGACCC
Found at i:20062 original size:45 final size:42
Alignment explanation
Indices: 19985--20070 Score: 145
Period size: 45 Copynumber: 2.0 Consensus size: 42
19975 TGTGTAGAAT
19985 TTTCTTTTATACAGTAATAAGATAGTAAGATAAGATAAGATA
1 TTTCTTTTATACAGTAATAAGATAGTAAGATAAGATAAGATA
20027 TTTCTTTTATACAGTAGCAGTAAGATAGTAAGATAAGATAAGAT
1 TTTCTTTTATACAGTA--A-TAAGATAGTAAGATAAGATAAGAT
20071 GAAAGTATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
42 16 0.39
44 1 0.02
45 24 0.59
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (42 bp):
TTTCTTTTATACAGTAATAAGATAGTAAGATAAGATAAGATA
Found at i:26986 original size:29 final size:29
Alignment explanation
Indices: 26923--26993 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
26913 ACATCGAACC
****
26923 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
* *
26952 GCCAAATAAGCCCCTGAACTCTTAAAAAA
1 GTCAAATAAGCCCCTGAACTATTAAAAAA
26981 GTCAAATAAGCCC
1 GTCAAATAAGCCC
26994 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAAAA
Found at i:28975 original size:65 final size:66
Alignment explanation
Indices: 28871--29003 Score: 250
Period size: 65 Copynumber: 2.0 Consensus size: 66
28861 TAAGACAACC
28871 TATCTCTACTTGAAAGAAGGTTTGCGATTTGAGTCTTGTCAATGGTCTTCGTTGATGAG-GATTG
1 TATCTCTACTTGAAAGAAGGTTTGCGATTTGAGTCTTGTCAATGGTCTTCGTTGATGAGTGATTG
28935 G
66 G
*
28936 TATCTCTACTTGAAAGAAGGTTTGCGATTTGAGTCTTGTCAATGGTCTTCGTTGGTGAGTGATTG
1 TATCTCTACTTGAAAGAAGGTTTGCGATTTGAGTCTTGTCAATGGTCTTCGTTGATGAGTGATTG
29001 G
66 G
29002 TA
1 TA
29004 AGTCTGTAAG
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 58 0.88
66 8 0.12
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (66 bp):
TATCTCTACTTGAAAGAAGGTTTGCGATTTGAGTCTTGTCAATGGTCTTCGTTGATGAGTGATTG
G
Found at i:30124 original size:3 final size:3
Alignment explanation
Indices: 30118--30146 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30108 TTTTCCTTTT
30118 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
30147 TAAAGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:31585 original size:35 final size:35
Alignment explanation
Indices: 31539--31610 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
31529 GTTGCTACTT
31539 AAAACTCTAAGTAGATATTAGGTGGAACCATTATG
1 AAAACTCTAAGTAGATATTAGGTGGAACCATTATG
31574 AAAACTCTAAGTAGATATTAGGTGGAACCATTATG
1 AAAACTCTAAGTAGATATTAGGTGGAACCATTATG
31609 AA
1 AA
31611 TCAATTCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (35 bp):
AAAACTCTAAGTAGATATTAGGTGGAACCATTATG
Found at i:37936 original size:36 final size:36
Alignment explanation
Indices: 37892--37967 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
37882 TTTGGAAGGG
37892 TTCT-ATATTTTATTGTCCTTTATCCCCATTTTCTT
1 TTCTCATATTTTATTGTCCTTTATCCCCATTTTCTT
37927 TTCTCATATTTTATTGTCCTTTATCCCCATTTTCTT
1 TTCTCATATTTTATTGTCCTTTATCCCCATTTTCTT
37963 TTCTC
1 TTCTC
37968 TCAGCTTGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 4 0.10
36 36 0.90
ACGTcount: A:0.13, C:0.25, G:0.03, T:0.59
Consensus pattern (36 bp):
TTCTCATATTTTATTGTCCTTTATCCCCATTTTCTT
Found at i:37958 original size:21 final size:21
Alignment explanation
Indices: 37898--37959 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
37888 AGGGTTCTAT
37898 ATTTTATTGTCCTTTATCCCC
1 ATTTTATTGTCCTTTATCCCC
* * *
37919 ATTTTCTT-TTC-TCAT----
1 ATTTTATTGTCCTTTATCCCC
37934 ATTTTATTGTCCTTTATCCCC
1 ATTTTATTGTCCTTTATCCCC
37955 ATTTT
1 ATTTT
37960 CTTTTCTCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 12
0.62 0.13 0.26
Matches are distributed among these distances:
15 7 0.24
16 2 0.07
17 3 0.10
19 3 0.10
20 2 0.07
21 12 0.41
ACGTcount: A:0.15, C:0.24, G:0.03, T:0.58
Consensus pattern (21 bp):
ATTTTATTGTCCTTTATCCCC
Found at i:55517 original size:13 final size:13
Alignment explanation
Indices: 55501--55535 Score: 63
Period size: 12 Copynumber: 2.8 Consensus size: 13
55491 ACAAAACGAG
55501 AGAAAAAAAAGAA
1 AGAAAAAAAAGAA
55514 AG-AAAAAAAGAA
1 AGAAAAAAAAGAA
55526 AGAAAAAAAA
1 AGAAAAAAAA
55536 AGAAGAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:55541 original size:13 final size:13
Alignment explanation
Indices: 55503--55543 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 13
55493 AAAACGAGAG
55503 AAAAAAAAGAA-A
1 AAAAAAAAGAAGA
*
55515 GAAAAAAAGAAAGA
1 AAAAAAAAG-AAGA
55529 AAAAAAAAGAAGA
1 AAAAAAAAGAAGA
55542 AA
1 AA
55544 TTAGAATTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.32
13 8 0.32
14 9 0.36
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAGA
Found at i:58621 original size:6 final size:6
Alignment explanation
Indices: 58612--58643 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
58602 GAAAAAATGA
58612 AAAAAG AAAAAG AAAAAG -AAAAG -AAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
58644 GCAGGCTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:58633 original size:11 final size:11
Alignment explanation
Indices: 58612--58644 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
58602 GAAAAAATGA
58612 AAAAAGAAAAAG
1 AAAAAG-AAAAG
58624 AAAAAGAAAAG
1 AAAAAGAAAAG
58635 -AAAAGAAAAG
1 AAAAAGAAAAG
58645 CAGGCTGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 5 0.24
12 6 0.29
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:64099 original size:24 final size:23
Alignment explanation
Indices: 64061--64106 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
64051 CTAACTCATT
64061 AAAAAAAAAAGAAAAAAAAGGAG
1 AAAAAAAAAAGAAAAAAAAGGAG
*
64084 AAAAGAAAAAGAAAAAGAAAGGA
1 AAAAAAAAAAGAAAAA-AAAGGA
64107 ACAACAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAGAAAAAAAAGGAG
Found at i:64103 original size:12 final size:11
Alignment explanation
Indices: 64061--64099 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
64051 CTAACTCATT
64061 AAAAAAAAAAG
1 AAAAAAAAAAG
*
64072 AAAAAAAAGGAG
1 AAAAAAAA-AAG
*
64084 AAAAGAAAAAG
1 AAAAAAAAAAG
64095 AAAAA
1 AAAAA
64100 GAAAGGAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Done.